Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 49
Found at i:6109008 original size:31 final size:32
Alignment explanation
Indices: 6108965--6109097 Score: 100
Period size: 31 Copynumber: 4.2 Consensus size: 32
6108955 ATATAATACA
**
6108965 TATATTTCAAAAATA-TTTTTTAAACTATATAT
1 TATATTTCAAAAA-AGTTTTCAAAACTATATAT
6108997 TATATTT-AAAAAAGTTTTCAAAACTATAT-T
1 TATATTTCAAAAAAGTTTTCAAAACTATATAT
* *
6109027 ATATAGTTTTC-AAAATGTTTT-AAAAATAT-TA-
1 -TATA--TTTCAAAAAAGTTTTCAAAACTATATAT
* *
6109058 TATAAGTTTTAAAAAACGTTTTTAAAACTATATAT
1 TAT-A-TTTCAAAAAA-GTTTTCAAAACTATATAT
6109093 TATAT
1 TATAT
6109098 AATTTATTCA
Statistics
Matches: 81, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
30 8 0.10
31 28 0.35
32 19 0.23
33 20 0.25
34 3 0.04
35 3 0.04
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATTTCAAAAAAGTTTTCAAAACTATATAT
Found at i:6109096 original size:37 final size:37
Alignment explanation
Indices: 6108969--6109280 Score: 300
Period size: 38 Copynumber: 8.8 Consensus size: 37
6108959 AATACATATA
* *
6108969 TTTCAAAAATATTTTTTAAACTATATA-T-TAT-A--
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
6109001 TTT-AAAAAAGTTTTCAAAACTATA--TTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
6109034 TTTC-AAAATG-TTTT-AAA--A-ATATTATATAAGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* * *
6109065 TTTAAAAAACGTTTTTAAAACTATATATTATATAATT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
6109102 TATTCAAAAATGTTTTTAAAACTACATATTATATAATT
1 T-TTCAAAAATGTTTTTAAAACTATATATTATATAAGT
6109140 TATTCAAAAATGTTTTTAAAACTATATATTATATAAGT
1 T-TTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* * * *
6109178 TTT-TAAAATGATTTTAAAATTATATGTTATATATA-T
1 TTTCAAAAATGTTTTTAAAACTATATATTATATA-AGT
* * *
6109214 TTTCTAAAATGTTTTAAAAACTATATGTTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
6109250 TTTCAAAAATATTTTAAAAAACTATATATTA
1 TTTCAAAAATGTTTT-TAAAACTATATATTA
6109281 CCCATATTTT
Statistics
Matches: 237, Mismatches: 24, Indels: 33
0.81 0.08 0.11
Matches are distributed among these distances:
28 1 0.00
29 1 0.00
30 7 0.03
31 30 0.13
32 11 0.05
33 12 0.05
34 3 0.01
35 1 0.00
36 45 0.19
37 56 0.24
38 70 0.30
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
Found at i:6109118 original size:38 final size:36
Alignment explanation
Indices: 6108954--6109301 Score: 287
Period size: 38 Copynumber: 9.8 Consensus size: 36
6108944 TAATATAAAT
* * * * *
6108954 TATATAATACATATATTTCAAAAATATTTTTTAAAC
1 TATATATTATATATTTTTCAAAAATGTTTTTAAAAC
* *
6108990 TATATA-T-TATA--TTT-AAAAAAGTTTTCAAAAC
1 TATATATTATATATTTTTCAAAAATGTTTTTAAAAC
* *
6109021 --TATATTATATAGTTTTC-AAAATG-TTTTAAAAA
1 TATATATTATATATTTTTCAAAAATGTTTTTAAAAC
* * *
6109053 TAT-TA-TATA-AGTTTTAAAAAACGTTTTTAAAAC
1 TATATATTATATATTTTTCAAAAATGTTTTTAAAAC
6109086 TATATATTATATAATTTATTCAAAAATGTTTTTAAAAC
1 TATATATTATAT-ATTT-TTCAAAAATGTTTTTAAAAC
*
6109124 TACATATTATATAATTTATTCAAAAATGTTTTTAAAAC
1 TATATATTATAT-ATTT-TTCAAAAATGTTTTTAAAAC
* *
6109162 TATATATTATATAAGTTTTT--AAAATGATTTTAAAAT
1 TATATATTATAT-A-TTTTTCAAAAATGTTTTTAAAAC
* * *
6109198 TATATGTTATATATATTTTCTAAAATGTTTTAAAAAC
1 TATATATTATATAT-TTTTCAAAAATGTTTTTAAAAC
* * * *
6109235 TATATGTTATATAGTTTTCAAAAATATTTTAAAAAAC
1 TATATATTATATATTTTTCAAAAATGTTTT-TAAAAC
*
6109272 TATATATTACCCATA-TTTTC-AAAATGTTTT
1 TATATATTA--TATATTTTTCAAAAATGTTTT
6109302 CTTTTTTAAA
Statistics
Matches: 263, Mismatches: 28, Indels: 41
0.79 0.08 0.12
Matches are distributed among these distances:
29 4 0.02
30 1 0.00
31 23 0.09
32 19 0.07
33 21 0.08
34 7 0.03
35 10 0.04
36 45 0.17
37 52 0.20
38 75 0.29
39 6 0.02
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
TATATATTATATATTTTTCAAAAATGTTTTTAAAAC
Found at i:6111079 original size:2 final size:2
Alignment explanation
Indices: 6111074--6111138 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
6111064 CTTACACCAA
6111074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6111116 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
6111139 GAAAAGCAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6111608 original size:16 final size:17
Alignment explanation
Indices: 6111570--6111617 Score: 71
Period size: 16 Copynumber: 2.8 Consensus size: 17
6111560 TGTTTATGAG
*
6111570 GGAATTGAAATCTGTGAA
1 GGAATTGGAATCTGT-AA
6111588 GGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
6111604 GGAATTGGAATCTG
1 GGAATTGGAATCTG
6111618 AAATCTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 15 0.52
18 14 0.48
ACGTcount: A:0.33, C:0.06, G:0.31, T:0.29
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:6112287 original size:32 final size:31
Alignment explanation
Indices: 6112207--6112287 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 31
6112197 CCTAAACCCG
**
6112207 AACTGACCTGAACCCGAAATTTTTTTTAAAAA
1 AACTGACCTG-ACCCGAAATTTTTTGAAAAAA
* *
6112239 ATCCGA-CTCGATCCCGAAATTTTTTGAAAAAA
1 AACTGACCT-GA-CCCGAAATTTTTTGAAAAAA
6112271 AACTTGACCTGACCCGA
1 AAC-TGACCTGACCCGA
6112288 CCCGAATATC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
31 3 0.08
32 30 0.77
33 4 0.10
34 2 0.05
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.27
Consensus pattern (31 bp):
AACTGACCTGACCCGAAATTTTTTGAAAAAA
Found at i:6112391 original size:32 final size:31
Alignment explanation
Indices: 6112326--6112392 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
6112316 CCCAAACCCG
*
6112326 AAATGTTTTAAAAAAATGTCCGACCGATCCCA
1 AAATGTTTTAAAAAAA-GTCCGACCGATACCA
*
6112358 AAATTTTTTAAAAAAA-TCCGACCCGAATACCA
1 AAATGTTTTAAAAAAAGTCCGA-CCG-ATACCA
6112390 AAA
1 AAA
6112393 GATTGATGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 5 0.16
31 3 0.10
32 23 0.74
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.24
Consensus pattern (31 bp):
AAATGTTTTAAAAAAAGTCCGACCGATACCA
Found at i:6113957 original size:16 final size:16
Alignment explanation
Indices: 6113938--6113969 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6113928 AGTAAGATTT
6113938 CATGTATTTAAGGTTC
1 CATGTATTTAAGGTTC
6113954 CATGTATTTAAGGTTC
1 CATGTATTTAAGGTTC
6113970 ACGTTTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (16 bp):
CATGTATTTAAGGTTC
Found at i:6114990 original size:19 final size:17
Alignment explanation
Indices: 6114956--6115000 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
6114946 AGAAATTCTT
*
6114956 TAAAAAATATATTTTTA
1 TAAAAAATATAGTTTTA
6114973 TAAAAAATCGATAGTTTTA
1 TAAAAAAT--ATAGTTTTA
*
6114992 TTAAAAATA
1 TAAAAAATA
6115001 AGAAATATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 9 0.38
19 15 0.62
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (17 bp):
TAAAAAATATAGTTTTA
Found at i:6118020 original size:59 final size:59
Alignment explanation
Indices: 6117898--6118020 Score: 142
Period size: 59 Copynumber: 2.1 Consensus size: 59
6117888 GTTGGATGAT
* * * *
6117898 CATTTTATAACTTTTAATAGTCGAGAGACTCAATAAAGCAACGTCTTATAATCGGAGAT
1 CATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAACATCTTATAATCAGAGAC
* * * *
6117957 CATTTTATAACTTTTAATAGTTGAG-GTACTCAACAAAGTAGCAATC-TATAGTCAGAGAC
1 CATTTTATAACTTTTAATAGTCGAGAG-ACTCAACAAAGCAAC-ATCTTATAATCAGAGAC
6118016 CATTT
1 CATTT
6118021 ATGTACTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
58 1 0.02
59 51 0.94
60 2 0.04
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (59 bp):
CATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAACATCTTATAATCAGAGAC
Found at i:6119061 original size:2 final size:2
Alignment explanation
Indices: 6119054--6119125 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
6119044 ATTCTAACTC
6119054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6119096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6119126 GAGTTTTACA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6119486 original size:14 final size:15
Alignment explanation
Indices: 6119460--6119489 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6119450 AGTTTACTTA
6119460 ATTTTTTATAAAAAT
1 ATTTTTTATAAAAAT
6119475 ATTTTTTA-AAAAAT
1 ATTTTTTATAAAAAT
6119489 A
1 A
6119490 AGAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTTATAAAAAT
Found at i:6119525 original size:21 final size:19
Alignment explanation
Indices: 6119492--6119535 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
6119482 AAAAAATAAG
*
6119492 AAAAAAATTTAAAATATTTA
1 AAAAAAATCTAAAATA-TTA
*
6119512 AAAAAAATACTAAATTATTA
1 AAAAAAAT-CTAAAATATTA
6119532 AAAA
1 AAAA
6119536 GTGATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAAAATCTAAAATATTA
Found at i:6119809 original size:20 final size:20
Alignment explanation
Indices: 6119777--6119814 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6119767 ATTAAAAATA
*
6119777 AAATTTTATAAA-TATTTAT
1 AAATTTTAAAAATTATTTAT
6119796 AAATTATTAAAAATTATTT
1 AAATT-TTAAAAATTATTT
6119815 TGAGAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 6 0.38
21 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATTTTAAAAATTATTTAT
Found at i:6120029 original size:18 final size:19
Alignment explanation
Indices: 6119995--6120031 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6119985 TTTAATGGGT
6119995 ACTCATTAATATTATTTTA
1 ACTCATTAATATTATTTTA
*
6120014 ACTCTTTAAT-TTATTTTA
1 ACTCATTAATATTATTTTA
6120032 GCATAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (19 bp):
ACTCATTAATATTATTTTA
Found at i:6120109 original size:15 final size:15
Alignment explanation
Indices: 6120091--6120120 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6120081 TATTATTTTT
*
6120091 TTTAATATTTTAATC
1 TTTAACATTTTAATC
6120106 TTTAACATTTTAATC
1 TTTAACATTTTAATC
6120121 AAAATAATCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAACATTTTAATC
Found at i:6124587 original size:19 final size:20
Alignment explanation
Indices: 6124547--6124592 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
6124537 ATTATAAACT
6124547 AAAAAATAAATATACAATATA
1 AAAAAATAAATATA-AATATA
6124568 AAAAAATAAATGATAAATA-A
1 AAAAAATAAAT-ATAAATATA
6124588 AAAAA
1 AAAAA
6124593 CAAGCGGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAAAATAAATATAAATATA
Found at i:6131957 original size:14 final size:14
Alignment explanation
Indices: 6131916--6131961 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
6131906 GTATAAAATA
*
6131916 TATATTTATATATG
1 TATATATATATATG
* * *
6131930 AATATGTATGTATG
1 TATATATATATATG
6131944 TATATATATATATG
1 TATATATATATATG
6131958 TATA
1 TATA
6131962 AAATCATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (14 bp):
TATATATATATATG
Found at i:6135772 original size:51 final size:51
Alignment explanation
Indices: 6135709--6135810 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
6135699 ATTTAAGCGC
* *
6135709 ACCATATAGATATTTCCTATCCTATGACCAACAAGCATAATATTATTCGAT
1 ACCATATAGATATTTCCTATCCTATAACCAACAAACATAATATTATTCGAT
*
6135760 ACCATATAGATATTTCCTATCCTATAACCAACAAACATAATCTTATTCGAT
1 ACCATATAGATATTTCCTATCCTATAACCAACAAACATAATATTATTCGAT
6135811 GCAATGTCCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (51 bp):
ACCATATAGATATTTCCTATCCTATAACCAACAAACATAATATTATTCGAT
Found at i:6139490 original size:54 final size:53
Alignment explanation
Indices: 6139408--6139513 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 53
6139398 GACTTATCAC
6139408 AACATTTAACTTCTATGCTCAAGAAATAACTTAGCTCACCTCAGTCTTTAAGAT
1 AACATTTAACTTCTATGCTCAAGAAATAACTT-GCTCACCTCAGTCTTTAAGAT
* *
6139462 AACATTTGACTTCTATGCTTAAGAAATAACTTGCTCACCTCAGTCTTTAAGA
1 AACATTTAACTTCTATGCTCAAGAAATAACTTGCTCACCTCAGTCTTTAAGA
6139514 GAACTTTTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 20 0.40
54 30 0.60
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (53 bp):
AACATTTAACTTCTATGCTCAAGAAATAACTTGCTCACCTCAGTCTTTAAGAT
Found at i:6141503 original size:3 final size:3
Alignment explanation
Indices: 6141490--6141522 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
6141480 TATTTATTTT
6141490 TTA TT- TTA TTA TTA TTAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
6141523 ATTTTACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6141513 original size:13 final size:13
Alignment explanation
Indices: 6141495--6141519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6141485 ATTTTTTATT
6141495 TTATTATTATTAA
1 TTATTATTATTAA
6141508 TTATTATTATTA
1 TTATTATTATTA
6141520 TTAATTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:6141514 original size:16 final size:16
Alignment explanation
Indices: 6141495--6141525 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6141485 ATTTTTTATT
6141495 TTATTATTATTAATTA
1 TTATTATTATTAATTA
6141511 TTATTATTATTAATT
1 TTATTATTATTAATT
6141526 TTACATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATTATTAATTA
Found at i:6141669 original size:25 final size:25
Alignment explanation
Indices: 6141640--6141763 Score: 223
Period size: 25 Copynumber: 5.0 Consensus size: 25
6141630 CCAACAACCC
*
6141640 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGTTTAGGGTTTCAAACCCTAA
6141665 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGTTTAGGGTTTCAAACCCTAA
6141690 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGTTTAGGGTTTCAAACCCTAA
6141715 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGTTTAGGGTTTCAAACCCTAA
*
6141740 ATCAATTTAGGGTTTC-AACCCTAA
1 ATCAGTTTAGGGTTTCAAACCCTAA
6141764 TCCCCTAACT
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
24 8 0.08
25 89 0.92
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (25 bp):
ATCAGTTTAGGGTTTCAAACCCTAA
Found at i:6142131 original size:27 final size:25
Alignment explanation
Indices: 6142086--6142147 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
6142076 ATAAAAGAAC
**
6142086 AAAAAAAGAAACCAGAAAAGGAGAG
1 AAAAAAAGAAACCAGAAAAAAAGAG
6142111 AAAAAAATCGAAA-CAGAAAAAAA-AG
1 AAAAAAA--GAAACCAGAAAAAAAGAG
6142136 AGAAAAAAGAAA
1 A-AAAAAAGAAA
6142148 GTTTTACCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
24 4 0.12
25 10 0.31
26 14 0.44
27 4 0.12
ACGTcount: A:0.74, C:0.06, G:0.18, T:0.02
Consensus pattern (25 bp):
AAAAAAAGAAACCAGAAAAAAAGAG
Found at i:6154669 original size:17 final size:18
Alignment explanation
Indices: 6154634--6154691 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
6154624 TAAAAAAAAA
6154634 AAAAAAAAAAAAAAGATG
1 AAAAAAAAAAAAAAGATG
**
6154652 AAAAAAAAAATGAA-ATG
1 AAAAAAAAAAAAAAGATG
** *
6154669 AAAAAATGAAAAAAGAAG
1 AAAAAAAAAAAAAAGATG
6154687 AAAAA
1 AAAAA
6154692 TAAATAAAGG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAAAAAAGATG
Found at i:6154672 original size:13 final size:12
Alignment explanation
Indices: 6154627--6154682 Score: 67
Period size: 13 Copynumber: 4.5 Consensus size: 12
6154617 TTACACTTAA
**
6154627 AAAAAAAAAAAA
1 AAAAAAAAAATG
6154639 AAAAAAAAAGATG
1 AAAAAAAAA-ATG
6154652 AAAAAAAAAATG
1 AAAAAAAAAATG
*
6154664 AAATGAAAAAATG
1 AAA-AAAAAAATG
6154677 AAAAAA
1 AAAAAA
6154683 GAAGAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
12 17 0.45
13 21 0.55
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (12 bp):
AAAAAAAAAATG
Found at i:6154692 original size:25 final size:25
Alignment explanation
Indices: 6154627--6154682 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
6154617 TTACACTTAA
* **
6154627 AAAAAAAAAAAAAAAAAAAAAGATG
1 AAAAAAAAAAGAAATGAAAAAGATG
6154652 AAAAAAAAAATGAAATGAAAAA-ATG
1 AAAAAAAAAA-GAAATGAAAAAGATG
6154677 AAAAAA
1 AAAAAA
6154683 GAAGAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (25 bp):
AAAAAAAAAAGAAATGAAAAAGATG
Found at i:6155914 original size:141 final size:141
Alignment explanation
Indices: 6155644--6155903 Score: 407
Period size: 141 Copynumber: 1.8 Consensus size: 141
6155634 AACATCAACT
6155644 GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
* * **
6155709 GGAACCGAGTTATCACCCTTCCTAACGATGGCCAGAGTTCTTCATCACGTATGAACCATGTCATC
66 GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
6155774 TATCCTTAGAC
131 TATCCTTAGAC
* * *
6155785 GACCAGA-CTTCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAATCAGCCGTCCTCATCACG
1 GACCAGATC-TCCTCATCACGTAGGAG-AGTGTCAACATTAGGATAACCAGCCGTCCTCATCACG
* *
6155848 TAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTATGA
64 TAGGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGA
6155904 GTCGTGTCAT
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
140 1 0.01
141 96 0.89
142 11 0.10
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (141 bp):
GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
TATCCTTAGAC
Found at i:6156179 original size:3 final size:3
Alignment explanation
Indices: 6156166--6156198 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
6156156 TATTTATTTT
6156166 TTA TT- TTA TTA TTA TTAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
6156199 ATTTTACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6156189 original size:13 final size:13
Alignment explanation
Indices: 6156171--6156195 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6156161 ATTTTTTATT
6156171 TTATTATTATTAA
1 TTATTATTATTAA
6156184 TTATTATTATTA
1 TTATTATTATTA
6156196 TTAATTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:6156190 original size:16 final size:16
Alignment explanation
Indices: 6156171--6156201 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6156161 ATTTTTTATT
6156171 TTATTATTATTAATTA
1 TTATTATTATTAATTA
6156187 TTATTATTATTAATT
1 TTATTATTATTAATT
6156202 TTACATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATTATTAATTA
Found at i:6156345 original size:25 final size:25
Alignment explanation
Indices: 6156316--6156439 Score: 223
Period size: 25 Copynumber: 5.0 Consensus size: 25
6156306 CCAACAACCC
*
6156316 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGTTTAGGGTTTCAAACCCTAA
6156341 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGTTTAGGGTTTCAAACCCTAA
6156366 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGTTTAGGGTTTCAAACCCTAA
6156391 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGTTTAGGGTTTCAAACCCTAA
*
6156416 ATCAATTTAGGGTTTC-AACCCTAA
1 ATCAGTTTAGGGTTTCAAACCCTAA
6156440 TCCCCTAACT
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
24 8 0.08
25 89 0.92
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (25 bp):
ATCAGTTTAGGGTTTCAAACCCTAA
Found at i:6156825 original size:26 final size:25
Alignment explanation
Indices: 6156762--6156825 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 25
6156752 ATAAAAGAAC
**
6156762 AAAAAAAGAAACCAGAAAAGGAGAG
1 AAAAAAAGAAACCAGAAAAAAAGAG
6156787 AAAAAAATCGAAA-CAGAAAAAAAAGAG
1 AAAAAAA--GAAACCAG-AAAAAAAGAG
6156814 AGAAAAAAGAAA
1 A-AAAAAAGAAA
6156826 GTTTTACCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 7 0.21
26 7 0.21
27 13 0.39
28 6 0.18
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.02
Consensus pattern (25 bp):
AAAAAAAGAAACCAGAAAAAAAGAG
Found at i:6160656 original size:16 final size:16
Alignment explanation
Indices: 6160627--6160709 Score: 134
Period size: 16 Copynumber: 5.3 Consensus size: 16
6160617 CGTTCATTTA
6160627 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
*
6160641 ATAAATAAACACGAAC
1 ATAAATGAACACGAAC
*
6160657 ATAAATGAACACGAAT
1 ATAAATGAACACGAAC
6160673 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
6160689 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
6160705 ATAAA
1 ATAAA
6160710 CGAATATAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
14 6 0.09
15 2 0.03
16 56 0.88
ACGTcount: A:0.60, C:0.16, G:0.10, T:0.14
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:6160722 original size:32 final size:32
Alignment explanation
Indices: 6160627--6160722 Score: 106
Period size: 32 Copynumber: 3.1 Consensus size: 32
6160617 CGTTCATTTA
** *
6160627 ATAAAT-AA-ACGAACATAAATAAACACGAAC
1 ATAAATGAACACGAACATAAACGAACACAAAC
* * *
6160657 ATAAATGAACACGAATATAAATGAACACGAAC
1 ATAAATGAACACGAACATAAACGAACACAAAC
* *
6160689 ATAAATGAACACGAACATAAACGAATATAAAC
1 ATAAATGAACACGAACATAAACGAACACAAAC
6160721 AT
1 AT
6160723 TGAAGACCCT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 6 0.11
31 2 0.04
32 49 0.86
ACGTcount: A:0.59, C:0.16, G:0.09, T:0.16
Consensus pattern (32 bp):
ATAAATGAACACGAACATAAACGAACACAAAC
Found at i:6161803 original size:10 final size:10
Alignment explanation
Indices: 6161788--6161866 Score: 68
Period size: 10 Copynumber: 7.5 Consensus size: 10
6161778 ATAAAAGAAT
6161788 GAACATAAAC
1 GAACATAAAC
6161798 GAACATAACCGAAC
1 GAACAT-A---AAC
*
6161812 AAACATAAAC
1 GAACATAAAC
*
6161822 GAACATAACC
1 GAACATAAAC
*
6161832 GAACATAACC
1 GAACATAAAC
*
6161842 GAACATAACC
1 GAACATAAAC
* *
6161852 GAACGTAAAT
1 GAACATAAAC
6161862 GAACA
1 GAACA
6161867 CAAAATCTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
10 48 0.83
11 1 0.02
13 1 0.02
14 8 0.14
ACGTcount: A:0.54, C:0.24, G:0.11, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:6161803 original size:24 final size:24
Alignment explanation
Indices: 6161775--6161829 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
6161765 GATTGGGTTA
**
6161775 AACATAAAAGAATGAACATAAACG
1 AACATAAAAGAACAAACATAAACG
**
6161799 AACATAACCGAACAAACATAAACG
1 AACATAAAAGAACAAACATAAACG
6161823 AACATAA
1 AACATAA
6161830 CCGAACATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.62, C:0.18, G:0.09, T:0.11
Consensus pattern (24 bp):
AACATAAAAGAACAAACATAAACG
Found at i:6161811 original size:20 final size:20
Alignment explanation
Indices: 6161788--6161866 Score: 95
Period size: 20 Copynumber: 3.8 Consensus size: 20
6161778 ATAAAAGAAT
6161788 GAACATAAACGAACATAACC
1 GAACATAAACGAACATAACC
6161808 GAACAAACATAAACGAACATAACC
1 G----AACATAAACGAACATAACC
*
6161832 GAACATAACCGAACATAACC
1 GAACATAAACGAACATAACC
* *
6161852 GAACGTAAATGAACA
1 GAACATAAACGAACA
6161867 CAAAATCTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
20 31 0.61
24 20 0.39
ACGTcount: A:0.54, C:0.24, G:0.11, T:0.10
Consensus pattern (20 bp):
GAACATAAACGAACATAACC
Found at i:6161830 original size:24 final size:23
Alignment explanation
Indices: 6161789--6161855 Score: 95
Period size: 24 Copynumber: 3.0 Consensus size: 23
6161779 TAAAAGAATG
6161789 AACATAAACGAACATAACCGAAC
1 AACATAAACGAACATAACCGAAC
6161812 AAACATAAACGAACATAACCG---
1 -AACATAAACGAACATAACCGAAC
*
6161833 AACATAACCGAACATAACCGAAC
1 AACATAAACGAACATAACCGAAC
6161856 GTAAATGAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
20 19 0.49
24 20 0.51
ACGTcount: A:0.55, C:0.27, G:0.09, T:0.09
Consensus pattern (23 bp):
AACATAAACGAACATAACCGAAC
Found at i:6161917 original size:40 final size:40
Alignment explanation
Indices: 6161857--6161936 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
6161847 TAACCGAACG
*
6161857 TAAATGAACACAAAATCTTGTTCATGTTCGTTCATTTAAT
1 TAAACGAACACAAAATCTTGTTCATGTTCGTTCATTTAAT
6161897 TAAACGAACACAAAATCTTGTTCATGTTCGTTCATTTAAT
1 TAAACGAACACAAAATCTTGTTCATGTTCGTTCATTTAAT
6161937 AAATAAACGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (40 bp):
TAAACGAACACAAAATCTTGTTCATGTTCGTTCATTTAAT
Found at i:6167849 original size:2 final size:2
Alignment explanation
Indices: 6167842--6167938 Score: 139
Period size: 2 Copynumber: 50.0 Consensus size: 2
6167832 CTAGATTTGA
6167842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
6167884 A- AT AT -T A- AT TT AT CCT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
6167923 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
6167939 TCGAATCATA
Statistics
Matches: 87, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
1 4 0.05
2 82 0.94
3 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6177244 original size:35 final size:36
Alignment explanation
Indices: 6177177--6177250 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
6177167 AAAGTAACCC
* * *
6177177 AAACTGAAGCAATCCGAACTAAAAAAATCTGAATTG
1 AAACCGAAGCAATACAAACTAAAAAAATCTGAATTG
6177213 AAACCGAAGCAATACAAACTAAAAAAA-CTGAATTG
1 AAACCGAAGCAATACAAACTAAAAAAATCTGAATTG
6177248 AAA
1 AAA
6177251 GTAACTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 11 0.31
36 24 0.69
ACGTcount: A:0.55, C:0.16, G:0.12, T:0.16
Consensus pattern (36 bp):
AAACCGAAGCAATACAAACTAAAAAAATCTGAATTG
Found at i:6179014 original size:11 final size:11
Alignment explanation
Indices: 6179000--6179035 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
6178990 GTAAAATTCA
6179000 TGAATTATAAG
1 TGAATTATAAG
6179011 TGAATTATAAG
1 TGAATTATAAG
6179022 TGAATTATAAG
1 TGAATTATAAG
6179033 TGA
1 TGA
6179036 GTGTTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.36
Consensus pattern (11 bp):
TGAATTATAAG
Found at i:6179525 original size:90 final size:90
Alignment explanation
Indices: 6179372--6179551 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
6179362 GGGGCGGTGC
*
6179372 ATTGAACCTCTTAGGAGGTATATGATCCCATTATGTTGGAGCAAATGCATATCAATTATTTTAGA
1 ATTGAACCTCTTAGGAGGTAAATGATCCCATTATGTTGGAGCAAATGCATATCAATTATTTTAGA
6179437 AAATTTATTAAATTTAACTTAGTAT
66 AAATTTATTAAATTTAACTTAGTAT
6179462 ATTGAACCTCTTAGGAGGTAAATGATCCCATTATGTTGGAGCAAATGCATATCAATTATTTTAGA
1 ATTGAACCTCTTAGGAGGTAAATGATCCCATTATGTTGGAGCAAATGCATATCAATTATTTTAGA
6179527 AAATTTATTAAATTTAACTTAGTAT
66 AAATTTATTAAATTTAACTTAGTAT
6179552 GTTAAGAGGA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (90 bp):
ATTGAACCTCTTAGGAGGTAAATGATCCCATTATGTTGGAGCAAATGCATATCAATTATTTTAGA
AAATTTATTAAATTTAACTTAGTAT
Found at i:6191825 original size:20 final size:20
Alignment explanation
Indices: 6191797--6191838 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
6191787 TTCTTCAAAC
*
6191797 GATCGATTCCCTAGCAGCAG
1 GATCCATTCCCTAGCAGCAG
6191817 GATCCATTCCCTAGCAGCAG
1 GATCCATTCCCTAGCAGCAG
6191837 GA
1 GA
6191839 ATCAAGCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19
Consensus pattern (20 bp):
GATCCATTCCCTAGCAGCAG
Found at i:6199381 original size:17 final size:17
Alignment explanation
Indices: 6199359--6199430 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
6199349 AAAACAAAAG
*
6199359 TAAAAGATATAGAACAA
1 TAAAAGATATAGTACAA
*
6199376 TAAAAGATACAGTACAA
1 TAAAAGATATAGTACAA
* * *
6199393 TAAGAGAAATAGTATAA
1 TAAAAGATATAGTACAA
*
6199410 TAAAAGAAATTA-TACAA
1 TAAAAGATA-TAGTACAA
6199427 TAAA
1 TAAA
6199431 TTAATCATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
17 44 0.96
18 2 0.04
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (17 bp):
TAAAAGATATAGTACAA
Found at i:6202722 original size:23 final size:23
Alignment explanation
Indices: 6202688--6202771 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
6202678 CAATTTTATA
*
6202688 TGGCACTACGGTGCAACTCTACG
1 TGGCACTTCGGTGCAACTCTACG
6202711 TGGCACTTCGGTGCAACTCTACG
1 TGGCACTTCGGTGCAACTCTACG
* *
6202734 TGGCACTTCGGTGCAATTTTACG
1 TGGCACTTCGGTGCAACTCTACG
*
6202757 TGACACTTCGGTGCA
1 TGGCACTTCGGTGCA
6202772 TTTATACGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.27
Consensus pattern (23 bp):
TGGCACTTCGGTGCAACTCTACG
Found at i:6203142 original size:18 final size:18
Alignment explanation
Indices: 6203101--6203146 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
6203091 ATAAATGGGT
6203101 TAATGATAATGATAGAGA
1 TAATGATAATGATAGAGA
* *
6203119 TTATGATAATGAT-GTTGA
1 TAATGATAATGATAG-AGA
6203137 TAATGATAAT
1 TAATGATAAT
6203147 ATATGTGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (18 bp):
TAATGATAATGATAGAGA
Found at i:6209602 original size:74 final size:74
Alignment explanation
Indices: 6209476--6209632 Score: 199
Period size: 74 Copynumber: 2.1 Consensus size: 74
6209466 TCAGTTCTTG
* ** * *
6209476 CAAAGCTTTAGATTTGTCTTAAACCAAAGTCTCTGCATGACAAGAAGAAATAAATCAGAGCTTGA
1 CAAAGCTATAGATTTGTCTTAAACCAAAGTCTCCACATGACAAGAAGAAATAAAGCAAAGCTTGA
*
6209541 TACAAATGC
66 CACAAATGC
* * *
6209550 CAAAGCTATAGAATTT-TCTTAAACCAGAGTCTCCACATGACGAGAAGCAATAAAGCAAAGCTTG
1 CAAAGCTATAG-ATTTGTCTTAAACCAAAGTCTCCACATGACAAGAAGAAATAAAGCAAAGCTTG
* *
6209614 ACGCAAATGT
65 ACACAAATGC
6209624 CAAAGCTAT
1 CAAAGCTAT
6209633 GACATTGTGA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
74 67 0.94
75 4 0.06
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (74 bp):
CAAAGCTATAGATTTGTCTTAAACCAAAGTCTCCACATGACAAGAAGAAATAAAGCAAAGCTTGA
CACAAATGC
Found at i:6211174 original size:40 final size:40
Alignment explanation
Indices: 6211119--6211199 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
6211109 ATTTCTTTGA
6211119 GCTAAAATGTTTAAACCCAAGTATTGGATATAAGGTCATT
1 GCTAAAATGTTTAAACCCAAGTATTGGATATAAGGTCATT
6211159 GCTAAAATGTTTAAACCCAAGTATTGGATATAAGGTCATT
1 GCTAAAATGTTTAAACCCAAGTATTGGATATAAGGTCATT
6211199 G
1 G
6211200 AGTAGCCTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (40 bp):
GCTAAAATGTTTAAACCCAAGTATTGGATATAAGGTCATT
Found at i:6211996 original size:3 final size:3
Alignment explanation
Indices: 6211988--6212018 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6211978 GTAAAAACTA
6211988 AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6212019 ATGTGAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:6213314 original size:3 final size:3
Alignment explanation
Indices: 6213283--6213341 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
6213273 AACGGGAAAA
* * *
6213283 AAT AA- AAT AA- AAT AAGT GAT AAA AAT AAT AAT AAAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT -AAT AAT AAT AAT
6213328 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
6213342 ATATAAAAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.80
4 5 0.11
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:6213333 original size:12 final size:11
Alignment explanation
Indices: 6213281--6213338 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
6213271 GAAACGGGAA
6213281 AAAATAA-AAT
1 AAAATAATAAT
*
6213291 AAAATAAGTGAT
1 AAAATAA-TAAT
6213303 AAAAATAATAAT
1 -AAAATAATAAT
*
6213315 -AAATAATGAT
1 AAAATAATAAT
6213325 AATAATAATAAT
1 AA-AATAATAAT
6213337 AA
1 AA
6213339 TAAATATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 16 0.41
11 1 0.03
12 15 0.38
13 7 0.18
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:6213461 original size:32 final size:32
Alignment explanation
Indices: 6213420--6213485 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
6213410 TAAAAAAACA
*
6213420 TTTTAAAAAACTATATAATTTTCAAAAATGTT
1 TTTTAAAAAACCATATAATTTTCAAAAATGTT
* *
6213452 TTTTTAAAAACCATATAATTTTTAAAAATGTT
1 TTTTAAAAAACCATATAATTTTCAAAAATGTT
6213484 TT
1 TT
6213486 AAAAATTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (32 bp):
TTTTAAAAAACCATATAATTTTCAAAAATGTT
Found at i:6213516 original size:36 final size:36
Alignment explanation
Indices: 6213471--6213724 Score: 221
Period size: 37 Copynumber: 6.9 Consensus size: 36
6213461 ACCATATAAT
* *
6213471 TTTTAAAAATGTTTTAAAAATTACATATTATATATG
1 TTTTCAAAATGTTTTAAAAATTATATATTATATATG
* *
6213507 CTTTCAAAATGTTTTTCAAAAAATTATATATTATATATTAA
1 TTTTCAAAATG-TTTT--AAAAATTATATATTATATA-T-G
* * *
6213548 TTTTCAAAACGTTTTAAAAACTATATA--ATATATA
1 TTTTCAAAATGTTTTAAAAATTATATATTATATATG
* * * *
6213582 TTTTCAAAAATGTTTTGAAAACTATATATTATATTTC
1 TTTTC-AAAATGTTTTAAAAATTATATATTATATATG
* * *
6213619 TTTTCAAAAACGTTTT-AAAACTATATAATATATAAATG
1 TTTTC-AAAATGTTTTAAAAATTATAT-AT-TATATATG
* * *
6213657 TTTTTAAAATGTTTTAAAAACTATATA-T-CATATG
1 TTTTCAAAATGTTTTAAAAATTATATATTATATATG
* *
6213691 TTTTCAAAATGTTTTCAAAATTATATAATATATA
1 TTTTCAAAATGTTTTAAAAATTATATATTATATA
6213725 AATTAAAAAA
Statistics
Matches: 182, Mismatches: 23, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
34 34 0.19
35 23 0.13
36 27 0.15
37 36 0.20
38 30 0.16
39 18 0.10
40 5 0.03
41 9 0.05
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTCAAAATGTTTTAAAAATTATATATTATATATG
Found at i:6213696 original size:72 final size:72
Alignment explanation
Indices: 6213548--6213728 Score: 235
Period size: 72 Copynumber: 2.5 Consensus size: 72
6213538 TATATATTAA
*
6213548 TTTTCAAAACGTTTTAAAAACTATATAATATAT--ATTTTCAAAAATGTTTTGAAAACTATATAT
1 TTTTCAAAACGTTTTAAAAACTATATAATATATAAATTTTCAAAAATGTTTTAAAAACTATATAT
*
6213611 TATATTTC
66 CATA-TTC
**
6213619 TTTTCAAAAACGTTTT-AAAACTATATAATATATAAATGTTTTTAAAATGTTTTAAAAACTATAT
1 TTTTC-AAAACGTTTTAAAAACTATATAATATATAAAT-TTTCAAAAATGTTTTAAAAACTATAT
*
6213683 ATCATA-TG
64 ATCATATTC
* * *
6213691 TTTTCAAAATGTTTTCAAAATTATATAATATATAAATT
1 TTTTCAAAACGTTTTAAAAACTATATAATATATAAATT
6213729 AAAAAAATAT
Statistics
Matches: 98, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
71 32 0.33
72 36 0.37
73 2 0.02
74 28 0.29
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (72 bp):
TTTTCAAAACGTTTTAAAAACTATATAATATATAAATTTTCAAAAATGTTTTAAAAACTATATAT
CATATTC
Found at i:6213704 original size:11 final size:11
Alignment explanation
Indices: 6213652--6213711 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
6213642 TATAATATAT
*
6213652 AAATGTTTTTA
1 AAATGTTTTCA
*
6213663 AAATGTTTTAA
1 AAATGTTTTCA
* *
6213674 AAACTATATATC-
1 AAA-TGT-TTTCA
*
6213686 ATATGTTTTCA
1 AAATGTTTTCA
6213697 AAATGTTTTCA
1 AAATGTTTTCA
6213708 AAAT
1 AAAT
6213712 TATATAATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 3 0.08
11 29 0.76
12 4 0.11
13 2 0.05
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:6214519 original size:164 final size:165
Alignment explanation
Indices: 6214335--6215093 Score: 959
Period size: 164 Copynumber: 4.6 Consensus size: 165
6214325 AAGTTGAATA
*
6214335 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * *
6214400 TCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAG
66 CCCTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAG
* *
6214465 TTGTGCTGCAAATGATATGCCCT-GGAGCTGAGCG
131 TTATGCTGCAAATGATATGCCCTCGAAGCTGAGCG
* ** *
6214499 TAGTCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAAGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* ** * *
6214564 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGA
66 CCCTTGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAA
* * *
6214628 GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
130 GTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCG
** *
6214664 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * *
6214729 -CCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAA
66 CCCTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAA
* * *
6214793 GTTATGCTGCAAATGACATG-CCTTGGAGCTGAGCG
130 GTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCG
* * * *
6214828 TAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * * * *
6214893 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAC
62 TGTGCCCTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGAC
* * *
6214958 TTAAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTG
126 TTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCG
* * * *
6214998 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGG
1 TAATCGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * *
6215063 TGTGCCCTCGAAGCTGAGTGTAATCGAACTC
62 TGTGCCCTTG-AGCTGAGCGTAGTCGAACTC
6215094 GGGGGTCTTT
Statistics
Matches: 529, Mismatches: 55, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
164 168 0.32
165 138 0.26
166 1 0.00
168 43 0.08
169 75 0.14
170 104 0.20
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (165 bp):
TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCCTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAG
TTATGCTGCAAATGATATGCCCTCGAAGCTGAGCG
Found at i:6214824 original size:249 final size:251
Alignment explanation
Indices: 6214358--6215149 Score: 948
Period size: 249 Copynumber: 3.2 Consensus size: 251
6214348 AGGTCTTTAG
* * * * * * * *
6214358 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTG-AGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
* * * * *
6214422 ACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCC
66 ACTCGAAGGTC--TTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT
** * *
6214487 TGGAGCTGAGCGTAGTCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTA
129 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTA
6214548 TGCTGCAAATGAAGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG-TCA
194 TGCTGCAAATGAAGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTCA
* * *
6214606 CAGATAACCCTTCT-AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 CAGATAACCCTTCTCA-ACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
** * *
6214670 AACTCGGGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTT
65 AACTCGAAGGTCTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT
*
6214733 GGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* **
6214798 GCTGCAAATGACA-TGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
195 GCTGCAAATGA-AGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCA
6214855 CAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
* *
6214920 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCC
66 ACTCGAAGGTC-TT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CC
* * * * *
6214985 TCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTT
128 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTT
** * * * * ***
6215050 ATGCTGCAAATGGTGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G--C-
193 ATGCTGCAAATGAAGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCA
* * * **
6215106 CAGATAGCCCTTCTCGACTTAAGCTATATTGCAAATGATGTGCC
1 CAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGCC
6215150 GTTGAGCTGG
Statistics
Matches: 470, Mismatches: 56, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
245 70 0.15
246 1 0.00
247 1 0.00
248 45 0.10
249 163 0.35
250 2 0.00
251 40 0.09
253 42 0.09
254 79 0.17
255 27 0.06
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (251 bp):
CAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
ACTCGAAGGTCTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTG
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGAAGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTCA
Found at i:6214953 original size:85 final size:85
Alignment explanation
Indices: 6214335--6215149 Score: 936
Period size: 84 Copynumber: 9.8 Consensus size: 85
6214325 AAGTTGAATA
* * *
6214335 TAATCGAACTCGAAGGTC--T--TTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * *
6214396 TGTGTCGTTG-AGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* * * * * *
6214415 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* *
6214480 TATGCCCT-GGAGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* ** * *
6214499 TAGTCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * *
6214560 AGTGCCGTTG-AGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* * ** * * * *
6214579 TAGTCGAACTCAAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
1 TAATCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
*
6214643 ATGTGCCCTCGAAGCTGAGTG
65 ATGTGCCCTCGAAGCTGAGCG
** * *
6214664 TAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * *
6214725 TATG-CCTTGGAGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* *
6214744 TAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
** * *
6214809 CATG-CCTTGGAGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* *
6214828 TAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
*
6214893 TGTGCCCTCGAAGCTGAGTG
66 TGTGCCCTCGAAGCTGAGCG
*
6214913 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
*
6214978 TGTGCCCTCGAAGCTGAGTG
66 TGTGCCCTCGAAGCTGAGCG
* *
6214998 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGG
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
*
6215063 TGTGCCCTCGAAGCTGAGTG
66 TGTGCCCTCGAAGCTGAGCG
** * * * **
6215083 TAATCGAACTCGGGGGTC--T--TTGCCAGATAGCCCTTCTCGACTTAAGCTATATTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
6215144 TGTGCC
66 TGTGCC
6215150 GTTGAGCTGG
Statistics
Matches: 635, Mismatches: 82, Indels: 35
0.84 0.11 0.05
Matches are distributed among these distances:
80 108 0.17
81 78 0.12
82 4 0.01
83 3 0.00
84 228 0.36
85 214 0.34
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (85 bp):
TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
TGTGCCCTCGAAGCTGAGCG
Found at i:6218384 original size:17 final size:19
Alignment explanation
Indices: 6218345--6218388 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
6218335 AGTTAATGTG
6218345 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
6218364 AATGCAAAGAAAAT-A-AA
1 AATGCAAAGAAAATAACAA
6218381 AATGCAAA
1 AATGCAAA
6218389 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 10 0.40
18 1 0.04
19 14 0.56
ACGTcount: A:0.68, C:0.09, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:6219024 original size:17 final size:17
Alignment explanation
Indices: 6218998--6219030 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6218988 TGCAAACGAT
*
6218998 GAACACAAAATAAAAGA
1 GAACAAAAAATAAAAGA
6219015 GAACAAAAAATAAAAG
1 GAACAAAAAATAAAAG
6219031 GGTTAGTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACAAAAAATAAAAGA
Found at i:6220068 original size:3 final size:3
Alignment explanation
Indices: 6220060--6220089 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
6220050 GTAAAAACTA
6220060 AAT AAT AAT AAT AAAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
6220090 ATGTGAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:6220074 original size:13 final size:13
Alignment explanation
Indices: 6220058--6220086 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6220048 TAGTAAAAAC
6220058 TAAATAATAATAA
1 TAAATAATAATAA
6220071 TAAATAATAATAA
1 TAAATAATAATAA
6220084 TAA
1 TAA
6220087 TAAATGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAATAATAATAA
Found at i:6220081 original size:16 final size:16
Alignment explanation
Indices: 6220060--6220091 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6220050 GTAAAAACTA
6220060 AATAATAATAATAAAT
1 AATAATAATAATAAAT
6220076 AATAATAATAATAAAT
1 AATAATAATAATAAAT
6220092 GTGAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAATAATAATAAAT
Found at i:6220233 original size:22 final size:18
Alignment explanation
Indices: 6220188--6220222 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
6220178 AATACCTACA
6220188 ATAAAATAAAAAAAAAAG
1 ATAAAATAAAAAAAAAAG
6220206 AT-AAATAAAAACAAAAA
1 ATAAAATAAAAA-AAAAA
6220223 AGGATCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (18 bp):
ATAAAATAAAAAAAAAAG
Found at i:6221379 original size:3 final size:3
Alignment explanation
Indices: 6221347--6221409 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
6221337 ACGGGAAAAA
*
6221347 AAT AA- AAT AA- AAT AAGT AAT AA- AA- AAT AAT AAT AAAT AAT GAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT AAT
6221390 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
6221410 ATATAAAAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 8 0.15
3 39 0.74
4 6 0.11
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:6221415 original size:9 final size:10
Alignment explanation
Indices: 6221351--6221412 Score: 76
Period size: 10 Copynumber: 6.5 Consensus size: 10
6221341 GAAAAAAATA
6221351 AAATAA-AAT
1 AAATAATAAT
* *
6221360 AAGTAATAAA
1 AAATAATAAT
6221370 AAATAATAAT
1 AAATAATAAT
*
6221380 AAATAATGAT
1 AAATAATAAT
6221390 -AATAATAAT
1 AAATAATAAT
6221399 -AATAATAAT
1 AAATAATAAT
6221408 AAATA
1 AAATA
6221413 TAAAAACTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
9 22 0.49
10 23 0.51
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (10 bp):
AAATAATAAT
Found at i:6221530 original size:32 final size:32
Alignment explanation
Indices: 6221489--6221554 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
6221479 AAAAAAAACA
*
6221489 TTTTAAAAAACTATATAATTTTCAAAAATGTT
1 TTTTAAAAAACCATATAATTTTCAAAAATGTT
* *
6221521 TTTTTAAAAACCATATAATTTTTAAAAATGTT
1 TTTTAAAAAACCATATAATTTTCAAAAATGTT
6221553 TT
1 TT
6221555 AAAAATTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (32 bp):
TTTTAAAAAACCATATAATTTTCAAAAATGTT
Found at i:6221677 original size:37 final size:36
Alignment explanation
Indices: 6221533--6221795 Score: 230
Period size: 37 Copynumber: 7.2 Consensus size: 36
6221523 TTTAAAAACC
* * *
6221533 ATATA-AT-TTTTAAAAATGTTTTAAAAATTACATA
1 ATATATATATTTTCAAAATGTTTTAAAAACTATATA
* ** *
6221567 TTATATATGCTTTCAAAATGTTTTTCAAAAAATTATATA
1 ATATATATATTTTCAAAATG-TTTT--AAAAACTATATA
* *
6221606 TTATATATTAATTTTCAAAACGTTTTAAAAACTATATA
1 ATATATA-T-ATTTTCAAAATGTTTTAAAAACTATATA
*
6221644 ATATATATATTTTCAAAAATGTTTTGAAAACTATATA
1 ATATATATATTTTC-AAAATGTTTTAAAAACTATATA
* * * **
6221681 TTATATTTCTTTTCAAAAACATTTT-AAAACTATATA
1 ATATATATATTTTC-AAAATGTTTTAAAAACTATATA
* *
6221717 ATATATAAATGTTTTTAAAATGTTTTAAAAACTATAT-
1 ATATAT--ATATTTTCAAAATGTTTTAAAAACTATATA
* * *
6221754 AT-CATATATTTTCAAAATGTTTTCAAAATTATATA
1 ATATATATATTTTCAAAATGTTTTAAAAACTATATA
6221789 ATATATA
1 ATATATA
6221796 AAAAAAATAT
Statistics
Matches: 188, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
34 29 0.15
35 4 0.02
36 36 0.19
37 55 0.29
38 32 0.17
39 18 0.10
40 5 0.03
41 9 0.05
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (36 bp):
ATATATATATTTTCAAAATGTTTTAAAAACTATATA
Found at i:6222773 original size:14 final size:14
Alignment explanation
Indices: 6222754--6222780 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6222744 AGACCAACTT
6222754 ACTTATATAATCAG
1 ACTTATATAATCAG
6222768 ACTTATATAATCA
1 ACTTATATAATCA
6222781 CTTCACTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
ACTTATATAATCAG
Found at i:6224526 original size:40 final size:40
Alignment explanation
Indices: 6224476--6224552 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
6224466 AATTTTGTAT
6224476 TTAAATTTAATTATAAAT-ATTTATAATA-TTATGATATCAA
1 TTAAATTTAATT-TAAATAATTTATAATAGTTAT-ATATCAA
* * *
6224516 TTAATTTTAATTTTAATAATTTATTATAGTTATATAT
1 TTAAATTTAATTTAAATAATTTATAATAGTTATATAT
6224553 ATATATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 4 0.12
40 24 0.75
41 4 0.12
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (40 bp):
TTAAATTTAATTTAAATAATTTATAATAGTTATATATCAA
Found at i:6226331 original size:2 final size:2
Alignment explanation
Indices: 6226324--6226374 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
6226314 TTGAAGTAAC
6226324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6226366 AT AT AT AT A
1 AT AT AT AT A
6226375 AAATTAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6230460 original size:3 final size:3
Alignment explanation
Indices: 6230452--6230497 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
6230442 ACGGTTAATT
6230452 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6230498 ATTTAAACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6231488 original size:57 final size:57
Alignment explanation
Indices: 6231416--6231524 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 57
6231406 CACAGGTTCC
* * * *
6231416 AAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGAATAGG
1 AAAATCGCAACGCTAATTACCGACATAGATAAACACTACTACCGCAACGCGAATAGG
* *
6231473 AAAATCGCAACGCTAATTACTGACATAGATAAACACTACTACCGTAACGCGA
1 AAAATCGCAACGCTAATTACCGACATAGATAAACACTACTACCGCAACGCGA
6231525 TTTTTAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (57 bp):
AAAATCGCAACGCTAATTACCGACATAGATAAACACTACTACCGCAACGCGAATAGG
Found at i:6231860 original size:12 final size:14
Alignment explanation
Indices: 6231827--6231856 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6231817 TTGTCGAATT
*
6231827 CGGATTTTTTTTAC
1 CGGATTTTTTCTAC
6231841 CGGATTTTTTCTAC
1 CGGATTTTTTCTAC
6231855 CG
1 CG
6231857 TTTTACCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (14 bp):
CGGATTTTTTCTAC
Found at i:6234829 original size:69 final size:69
Alignment explanation
Indices: 6234705--6234838 Score: 193
Period size: 69 Copynumber: 1.9 Consensus size: 69
6234695 AAGTTAACAT
* *
6234705 GGGATAATTATGATTAGGAGCTTCCGTGCTAGTCACTTTAATTATTCGGGACTCTCGTGCGAGAT
1 GGGATAATTATGATTAGGAGCTTCCGTGCGAGTCACTCTAATTATTCGGGACTCTCGTGCGAGAT
6234770 ACCC
66 ACCC
*
6234774 GGGATAATTATGATTAGGTG-TTCCCGTGCGAGTCACTCTAATCT-TTCAGGG-CTCTCGTGCGA
1 GGGATAATTATGATTAGGAGCTT-CCGTGCGAGTCACTCTAAT-TATTC-GGGACTCTCGTGCGA
6234836 GAT
63 GAT
6234839 TGTTGAATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
68 2 0.03
69 53 0.90
70 4 0.07
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (69 bp):
GGGATAATTATGATTAGGAGCTTCCGTGCGAGTCACTCTAATTATTCGGGACTCTCGTGCGAGAT
ACCC
Found at i:6235269 original size:21 final size:23
Alignment explanation
Indices: 6235245--6235291 Score: 80
Period size: 21 Copynumber: 2.1 Consensus size: 23
6235235 ATTATTTGAA
6235245 AAAGGGTCGATCCCTT-T-CATT
1 AAAGGGTCGATCCCTTGTGCATT
6235266 AAAGGGTCGATCCCTTGTGCATT
1 AAAGGGTCGATCCCTTGTGCATT
6235289 AAA
1 AAA
6235292 TGTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 16 0.67
22 1 0.04
23 7 0.29
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (23 bp):
AAAGGGTCGATCCCTTGTGCATT
Found at i:6235759 original size:2 final size:2
Alignment explanation
Indices: 6235754--6235793 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
6235744 GGTTTTTGAA
6235754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6235794 GTTTTTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6235826 original size:39 final size:39
Alignment explanation
Indices: 6235776--6236004 Score: 315
Period size: 39 Copynumber: 5.8 Consensus size: 39
6235766 ATATATATAT
6235776 ATATATATATAATATATAGTTTTTGAAAACATTTTTAAA
1 ATATATATATAATATATAGTTTTTGAAAACATTTTTAAA
*
6235815 ATATATATATAATATATAGTTTTTGAAAACATTTTAAAA
1 ATATATATATAATATATAGTTTTTGAAAACATTTTTAAA
*
6235854 ATATATATATAATATATAGTTTTTGAAAACA-TTTTGAA
1 ATATATATATAATATATAGTTTTTGAAAACATTTTTAAA
*
6235892 A-ATATACATAATATATAGTTTTTGAAAACATTTTGAATATATA
1 ATATATATATAATATATAGTTTTTGAAAACATTTT---TA-A-A
*
6235935 TATATATATATATATATATAGTTTTTGAAAACA-TTTTGAA
1 -ATATATATATA-ATATATAGTTTTTGAAAACATTTTTAAA
*
6235975 A-ATATATATAATATAT-GGTTTTGAAAACAT
1 ATATATATATAATATATAGTTTTTGAAAACAT
6236005 ATATAATATA
Statistics
Matches: 172, Mismatches: 8, Indels: 22
0.85 0.04 0.11
Matches are distributed among these distances:
36 12 0.07
37 34 0.20
38 18 0.10
39 70 0.41
40 1 0.01
41 2 0.01
42 2 0.01
43 1 0.01
44 1 0.01
45 11 0.06
46 20 0.12
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (39 bp):
ATATATATATAATATATAGTTTTTGAAAACATTTTTAAA
Found at i:6235935 original size:2 final size:2
Alignment explanation
Indices: 6235928--6235954 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6235918 AACATTTTGA
6235928 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6235955 GTTTTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6235980 original size:38 final size:37
Alignment explanation
Indices: 6235938--6236106 Score: 168
Period size: 38 Copynumber: 4.8 Consensus size: 37
6235928 ATATATATAT
*
6235938 ATATATATATATATATAGTTTTTGAAAACATTTTGAAA
1 ATATATATA-ATATATAGTTTTTGAAAATATTTTGAAA
6235976 ATATATATAATATAT-G-----G------TTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
*
6236001 ACATATATAATATATAG-TTTTGAAAATATTTTGAAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTG-AAA
6236038 CATATATATAATATATAGTTTTTGAAAATATTTTTGAAA
1 -ATATATATAATATATAGTTTTTGAAAATA-TTTTGAAA
* *
6236077 ATGTATATAATATATAGTTTTT-AAATTATT
1 ATATATATAATATATAGTTTTTGAAAATATT
6236107 ATTTAATTAT
Statistics
Matches: 112, Mismatches: 4, Indels: 32
0.76 0.03 0.22
Matches are distributed among these distances:
25 22 0.20
26 1 0.01
30 1 0.01
31 1 0.01
36 8 0.07
37 14 0.12
38 46 0.41
39 14 0.12
40 5 0.04
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
Found at i:6235999 original size:25 final size:25
Alignment explanation
Indices: 6235968--6236029 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
6235958 TTTGAAAACA
*
6235968 TTTTGAAAATATATATAATATATGG
1 TTTTGAAAATATATATAATATATAG
*
6235993 TTTTGAAAACATATATAATATATAG
1 TTTTGAAAATATATATAATATATAG
6236018 TTTTGAAAATAT
1 TTTTGAAAATAT
6236030 TTTGAAAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.44
Consensus pattern (25 bp):
TTTTGAAAATATATATAATATATAG
Found at i:6236033 original size:61 final size:66
Alignment explanation
Indices: 6235940--6236065 Score: 199
Period size: 63 Copynumber: 2.0 Consensus size: 66
6235930 ATATATATAT
6235940 ATATATATATATATAGTTTTTGAAAACATTTTG-AAA-ATATATATAATATAT-GGTTTTGAAAA
1 ATATATATATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATATATAGGTTTTGAAAA
6236002 C
66 C
* *
6236003 ATATATA-ATATATAG-TTTTGAAAATATTTTGAAAACATATATATAATATATAGTTTTTGAAAA
1 ATATATATATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATATATAGGTTTTGAAAA
6236066 TATTTTTGAA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
61 15 0.26
62 11 0.19
63 22 0.38
64 10 0.17
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (66 bp):
ATATATATATATATAGTTTTTGAAAACATTTTGAAAACATATATATAATATATAGGTTTTGAAAA
C
Found at i:6236088 original size:76 final size:75
Alignment explanation
Indices: 6235776--6236098 Score: 318
Period size: 83 Copynumber: 4.3 Consensus size: 75
6235766 ATATATATAT
*
6235776 ATATATATATAATATATAGTTTTTGAAAACATTTTTAAAATATATATATAATATATAGTTTTTGA
1 ATATATATATAATATATAGTTTTTGAAAACA-TTTTGAAA-ATATATATAATATATAGTTTTTGA
*
6235841 AAACATTTTAAAA
64 AAACATTTT-TAA
*
6235854 ATATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATACATAATATATAGTTTTTGAAA
1 ATATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAA
6235919 ACATTTTGAATATATA
66 ACA-TTT---T-TA-A
*
6235935 TATATATATATATATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATAT-GGTTTTGA
1 -ATATATATATA-ATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGA
* *
6235999 AAACATATAT-A
64 AAACATTTTTAA
*
6236010 ATATATAGTTTTGAA-A-ATA--TTTTGAAAAC---------ATATATATAATATATAGTTTTTG
1 ATATATA--TAT-AATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTG
*
6236062 AAAATATTTTTGAA
63 AAAACATTTTT-AA
*
6236076 A-ATGTATATAATATATAGTTTTT
1 ATATATATATAATATATAGTTTTT
6236099 AAATTATTAT
Statistics
Matches: 214, Mismatches: 14, Indels: 46
0.78 0.05 0.17
Matches are distributed among these distances:
62 2 0.01
63 18 0.08
64 17 0.08
65 4 0.02
66 6 0.03
72 10 0.05
74 10 0.05
75 2 0.01
76 31 0.14
77 12 0.06
78 31 0.14
80 3 0.01
81 3 0.01
82 23 0.11
83 42 0.20
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (75 bp):
ATATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAA
ACATTTTTAA
Found at i:6236267 original size:68 final size:69
Alignment explanation
Indices: 6236148--6236278 Score: 158
Period size: 68 Copynumber: 1.9 Consensus size: 69
6236138 AGTTACCTGG
* * ** * ** *
6236148 GATAATTATGATTAGGTGCTTCTGTGTTAGTCACTTTAATCCTTTGGGGCTCTCGTGCGAGATAG
1 GATAATTATGATTAAGTGCTTCCGTGCGAGTCACTCTAATCCTTTAAGGCTCTCATGCGAGATAG
6236213 TCGA
66 TCGA
*
6236217 GATAATTATGATTAAGTG-TTCCGTGCGAGTCACTCTAAT-CTTTCAAGGCTCTCATGTGAGAT
1 GATAATTATGATTAAGTGCTTCCGTGCGAGTCACTCTAATCCTTT-AAGGCTCTCATGCGAGAT
6236279 TGTTGAATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
67 4 0.08
68 31 0.60
69 17 0.33
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (69 bp):
GATAATTATGATTAAGTGCTTCCGTGCGAGTCACTCTAATCCTTTAAGGCTCTCATGCGAGATAG
TCGA
Found at i:6236351 original size:30 final size:30
Alignment explanation
Indices: 6236317--6236386 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
6236307 TTGTAAAATT
*
6236317 GATTTTAGGCTGAATTAAAATTATCAAAAA
1 GATTTTAGACTGAATTAAAATTATCAAAAA
* * * *
6236347 GATTTTAGACTTAGTTGAATTTATCAAAAA
1 GATTTTAGACTGAATTAAAATTATCAAAAA
6236377 GATTTTAGAC
1 GATTTTAGAC
6236387 ATAATCGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.37
Consensus pattern (30 bp):
GATTTTAGACTGAATTAAAATTATCAAAAA
Found at i:6236397 original size:30 final size:30
Alignment explanation
Indices: 6236337--6236405 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
6236327 TGAATTAAAA
* * *
6236337 TTATCAAAAAGATTTTAGACTTAGTTGAAT
1 TTATCAAAAAGATTTTAGACATAATCGAAT
6236367 TTATCAAAAAGATTTTAGACATAATCGAAT
1 TTATCAAAAAGATTTTAGACATAATCGAAT
6236397 TTATCAAAA
1 TTATCAAAA
6236406 TTTATCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (30 bp):
TTATCAAAAAGATTTTAGACATAATCGAAT
Found at i:6238460 original size:21 final size:21
Alignment explanation
Indices: 6238400--6238461 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
6238390 TTTTTCCAAA
* **
6238400 AAAAGGATCAATCCCTTTGCC
1 AAAAGGATCGATCCCTTTTTC
6238421 AAAAGGATCGATCCCTTTTTC
1 AAAAGGATCGATCCCTTTTTC
*
6238442 AAAAGTATCGATCCCTTTTT
1 AAAAGGATCGATCCCTTTTT
6238462 GTGAAAGATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (21 bp):
AAAAGGATCGATCCCTTTTTC
Found at i:6238472 original size:21 final size:20
Alignment explanation
Indices: 6238400--6238476 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
6238390 TTTTTCCAAA
* **
6238400 AAAAGGATCAATCCCTTTGCC
1 AAAA-GATCGATCCCTTTTTC
6238421 AAAAGGATCGATCCCTTTTTC
1 AAAA-GATCGATCCCTTTTTC
*
6238442 AAAAGTATCGATCCCTTTTTGT
1 AAAAG-ATCGATCCCTTTTT-C
*
6238464 GAAAGATCGATCC
1 AAAAGATCGATCC
6238477 ATTTAGGCCA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.90
22 4 0.08
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (20 bp):
AAAAGATCGATCCCTTTTTC
Found at i:6241331 original size:26 final size:21
Alignment explanation
Indices: 6241280--6241335 Score: 94
Period size: 22 Copynumber: 2.6 Consensus size: 21
6241270 ATAACTCAAA
6241280 GAATTAATATTTATTTAAATC
1 GAATTAATATTTATTTAAATC
6241301 GAATTAAATATTTATTTAAATC
1 GAATT-AATATTTATTTAAATC
*
6241323 GAATTAATTTTTA
1 GAATTAATATTTA
6241336 CCGCTACTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
21 12 0.36
22 21 0.64
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (21 bp):
GAATTAATATTTATTTAAATC
Found at i:6243270 original size:13 final size:13
Alignment explanation
Indices: 6243252--6243292 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
6243242 AGAAACTTTA
*
6243252 ATTTATAAGATAT
1 ATTTATAAAATAT
*
6243265 ATTTATAAAAAAT
1 ATTTATAAAATAT
6243278 AATTTATAAAATAT
1 -ATTTATAAAATAT
6243292 A
1 A
6243293 GTATAAATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
ATTTATAAAATAT
Found at i:6246189 original size:17 final size:18
Alignment explanation
Indices: 6246140--6246189 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
6246130 CATATGTCGC
*
6246140 ATTTATATAATTTTAAAAA
1 ATTTATA-AATTATAAAAA
6246159 ATTTATTAAA--ATAAAAA
1 ATTTA-TAAATTATAAAAA
6246176 ATTTA-AAATTATAA
1 ATTTATAAATTATAA
6246190 TTTTTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 3 0.11
17 15 0.56
19 7 0.26
20 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTATAAATTATAAAAA
Found at i:6246943 original size:30 final size:30
Alignment explanation
Indices: 6246907--6246974 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
6246897 CGGCATATCC
6246907 AGGTGTCTAACGTTACAAACGTTATCATTT
1 AGGTGTCTAACGTTACAAACGTTATCATTT
* * *
6246937 -GAGTGTCTAGCGTTACAAATGTTATTATTT
1 AG-GTGTCTAACGTTACAAACGTTATCATTT
6246967 AGGTGTCT
1 AGGTGTCT
6246975 CGGGCTAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 31 0.94
31 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (30 bp):
AGGTGTCTAACGTTACAAACGTTATCATTT
Found at i:6247567 original size:31 final size:31
Alignment explanation
Indices: 6247520--6247587 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
6247510 GTTAGAAACG
* ** *
6247520 AGACACTTAAAATAATAATGTTTGTAACATT
1 AGACACCTAAAATAATAACATTTATAACATT
* *
6247551 AGACACCTAAAGTAATAACATTTATAACTTT
1 AGACACCTAAAATAATAACATTTATAACATT
6247582 AGACAC
1 AGACAC
6247588 TTGTATGTGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.31
Consensus pattern (31 bp):
AGACACCTAAAATAATAACATTTATAACATT
Found at i:6248032 original size:16 final size:16
Alignment explanation
Indices: 6248011--6248042 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6248001 TATAAAATCT
6248011 AATAATTCATAATATA
1 AATAATTCATAATATA
*
6248027 AATAATTCATTATATA
1 AATAATTCATAATATA
6248043 TATATACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:6249494 original size:47 final size:47
Alignment explanation
Indices: 6249377--6249516 Score: 192
Period size: 47 Copynumber: 3.0 Consensus size: 47
6249367 CCATCTTTAG
* **
6249377 AAAGGGTGATAACACAGTTCCTACGTGATGAGGACAATTGGTTATCT
1 AAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATCT
* * * *
6249424 -GAGGGTGATAACACGGTTTCTACGTGATGAGGACGGCTAGTTATCT
1 AAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATCT
* *
6249470 AAAGGGTGATAACATGGTTCCTACGTGATGAGGGCGGTTGGTTATCT
1 AAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATCT
6249517 GGGGTAACAC
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
46 39 0.49
47 40 0.51
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (47 bp):
AAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATCT
Found at i:6251568 original size:15 final size:15
Alignment explanation
Indices: 6251550--6251584 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
6251540 TTTTTATTTT
6251550 ATTAATA-TATATTAA
1 ATTAATATTA-ATTAA
6251565 ATTAATATTAATTAA
1 ATTAATATTAATTAA
6251580 ATTAA
1 ATTAA
6251585 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAATATTAATTAA
Found at i:6255805 original size:15 final size:15
Alignment explanation
Indices: 6255785--6255817 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6255775 ATTTATATAT
*
6255785 ATATATATTTTAAAA
1 ATATATATATTAAAA
6255800 ATATATATATTAAAA
1 ATATATATATTAAAA
6255815 ATA
1 ATA
6255818 ATAAAGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATATATATTAAAA
Found at i:6256495 original size:30 final size:29
Alignment explanation
Indices: 6256461--6256523 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
6256451 ATCATTATCA
*
6256461 TTAACCCATTTAAAACATGTCATCTTGTAC
1 TTAACCC-TTTAAAACATGTCATCTTATAC
**
6256491 TTAA-CCTTTGTAACATGTCATCTTATAC
1 TTAACCCTTTAAAACATGTCATCTTATAC
6256519 TTAAC
1 TTAAC
6256524 ATTTGTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 23 0.79
29 2 0.07
30 4 0.14
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (29 bp):
TTAACCCTTTAAAACATGTCATCTTATAC
Found at i:6256505 original size:28 final size:28
Alignment explanation
Indices: 6256474--6256539 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
6256464 ACCCATTTAA
* *
6256474 AACATGTCATCTTGTACTTAACCTTTGT
1 AACATGTCATCTTATACTTAACATTTGT
6256502 AACATGTCATCTTATACTTAACATTTGT
1 AACATGTCATCTTATACTTAACATTTGT
*
6256530 AACATATCAT
1 AACATGTCAT
6256540 ATAATACATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.41
Consensus pattern (28 bp):
AACATGTCATCTTATACTTAACATTTGT
Found at i:6256546 original size:28 final size:28
Alignment explanation
Indices: 6256488--6256546 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
6256478 TGTCATCTTG
* * * *
6256488 TACTTAACCTTTGTAACATGTCATCTTA
1 TACTTAACATTTGTAACATATCATATAA
6256516 TACTTAACATTTGTAACATATCATATAA
1 TACTTAACATTTGTAACATATCATATAA
6256544 TAC
1 TAC
6256547 ATTTCACCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (28 bp):
TACTTAACATTTGTAACATATCATATAA
Found at i:6256855 original size:17 final size:17
Alignment explanation
Indices: 6256814--6256857 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
6256804 GTCATATGTG
* *
6256814 TCCCGAAAGACCTATCA
1 TCCCGAAGGACCTATAA
6256831 TCCCGAAGGACCTATAA
1 TCCCGAAGGACCTATAA
6256848 TCCCGAAGGA
1 TCCCGAAGGA
6256858 TGTAATCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (17 bp):
TCCCGAAGGACCTATAA
Found at i:6256878 original size:21 final size:21
Alignment explanation
Indices: 6256848--6256899 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
6256838 GGACCTATAA
*
6256848 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTAATATGTG
*
6256869 TCCTGAAGGATGTAATATGTG
1 TCCCGAAGGATGTAATATGTG
6256890 TCCCGAAGGA
1 TCCCGAAGGA
6256900 CCTATCATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (21 bp):
TCCCGAAGGATGTAATATGTG
Found at i:6257106 original size:33 final size:33
Alignment explanation
Indices: 6257059--6257123 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
6257049 ATCATGTAGC
6257059 TTGTATAACATTCTTGTATGATCTCATAGATCA
1 TTGTATAACATTCTTGTATGATCTCATAGATCA
*
6257092 TTGTGTAACATTCTTGTATGATCTCATAGATC
1 TTGTATAACATTCTTGTATGATCTCATAGATC
6257124 CCTTTTCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TTGTATAACATTCTTGTATGATCTCATAGATCA
Found at i:6258309 original size:30 final size:31
Alignment explanation
Indices: 6258253--6258311 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
6258243 AACCATTCCC
*
6258253 AACTTTTCCAAAATTACAGAATTGGTCCCCT
1 AACTTTTCAAAAATTACAGAATTGGTCCCCT
6258284 AACTTTTCAAAAATTACAGAA-TGGTCCC
1 AACTTTTCAAAAATTACAGAATTGGTCCC
6258312 AAAATTGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (31 bp):
AACTTTTCAAAAATTACAGAATTGGTCCCCT
Found at i:6259338 original size:30 final size:29
Alignment explanation
Indices: 6259264--6259338 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
6259254 AAAATTACAT
*
6259264 TTTG-GTCCCTAAACTTTTCAAAGTTTATA
1 TTTGAGTCACTAAAC-TTTCAAAGTTTATA
* * *
6259293 TTTTAGTCACCAAACTTTCAAATTCTTATAA
1 TTTGAGTCACTAAACTTTCAAAGT-TTAT-A
6259324 TTTGA-TCACTAAACT
1 TTTGAGTCACTAAACT
6259339 ACATCCATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
29 11 0.30
30 21 0.57
31 5 0.14
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.43
Consensus pattern (29 bp):
TTTGAGTCACTAAACTTTCAAAGTTTATA
Found at i:6260515 original size:11 final size:13
Alignment explanation
Indices: 6260496--6260527 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
6260486 TATAAATAAA
6260496 TATAAATAT-TTT
1 TATAAATATATTT
6260508 TA-AAATATATTT
1 TATAAATATATTT
6260520 TATAAATA
1 TATAAATA
6260528 AATTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 7 0.39
13 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATAAATATATTT
Found at i:6260665 original size:6 final size:6
Alignment explanation
Indices: 6260654--6260680 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6260644 GAAAAACAAC
6260654 AGCAAT AGCAAT AGCAAT AGCAAT AGC
1 AGCAAT AGCAAT AGCAAT AGCAAT AGC
6260681 GAGGGGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.15
Consensus pattern (6 bp):
AGCAAT
Found at i:6260734 original size:7 final size:7
Alignment explanation
Indices: 6260681--6260731 Score: 84
Period size: 7 Copynumber: 7.3 Consensus size: 7
6260671 TAGCAATAGC
6260681 GAGGGGA
1 GAGGGGA
6260688 GAGGGGA
1 GAGGGGA
6260695 GAGGGGA
1 GAGGGGA
6260702 GAGGGGA
1 GAGGGGA
6260709 GAGGGGA
1 GAGGGGA
*
6260716 GAAGGGA
1 GAGGGGA
*
6260723 GAAGGGA
1 GAGGGGA
6260730 GA
1 GA
6260732 AGGTGGTTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (7 bp):
GAGGGGA
Found at i:6264663 original size:24 final size:23
Alignment explanation
Indices: 6264636--6264722 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
6264626 ATTTCCTAAT
*
6264636 TGAATTATGTTCTGATACGTTACA
1 TGAATTATGTTCTGATAC-TGACA
* * *
6264660 TGAATTCTGTTCTGATTCTGATA
1 TGAATTATGTTCTGATACTGACA
* *
6264683 TGGATTATGTTCTGATATCTGATA
1 TGAATTATGTTCTGATA-CTGACA
* *
6264707 TGAATTCTGTTTTGAT
1 TGAATTATGTTCTGAT
6264723 TTCTGATATC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 17 0.33
24 35 0.67
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.47
Consensus pattern (23 bp):
TGAATTATGTTCTGATACTGACA
Found at i:6264690 original size:47 final size:48
Alignment explanation
Indices: 6264622--6264731 Score: 136
Period size: 47 Copynumber: 2.3 Consensus size: 48
6264612 AAATATTTTA
* * *
6264622 TCTGATTTCCTAAT-TGAATTATGTTCTGATA-CGTTACATGAATTCTGT
1 TCTGATTT-CTGATATGGATTATGTTCTGATATC-TGACATGAATTCTGT
*
6264670 TCTGA-TTCTGATATGGATTATGTTCTGATATCTGATATGAATTCTGT
1 TCTGATTTCTGATATGGATTATGTTCTGATATCTGACATGAATTCTGT
*
6264717 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
6264732 CTCCGTTTAC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
46 4 0.07
47 35 0.65
48 15 0.28
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATATGGATTATGTTCTGATATCTGACATGAATTCTGT
Found at i:6264727 original size:24 final size:24
Alignment explanation
Indices: 6264659--6264731 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
6264649 GATACGTTAC
6264659 ATGAATTCTGTTCTGA-TTCTGAT
1 ATGAATTCTGTTCTGATTTCTGAT
* * *
6264682 ATGGATTATGTTCTGATATCTGAT
1 ATGAATTCTGTTCTGATTTCTGAT
*
6264706 ATGAATTCTGTTTTGATTTCTGAT
1 ATGAATTCTGTTCTGATTTCTGAT
6264730 AT
1 AT
6264732 CTCCGTTTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 14 0.33
24 28 0.67
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (24 bp):
ATGAATTCTGTTCTGATTTCTGAT
Found at i:6264917 original size:2 final size:2
Alignment explanation
Indices: 6264912--6264941 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6264902 TATGCTTTAA
6264912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6264942 CTTTTTACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6271626 original size:24 final size:24
Alignment explanation
Indices: 6271589--6271635 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
6271579 ATATTATTTC
6271589 TTCTCCTAAAATTTTATAAGTTCA
1 TTCTCCTAAAATTTTATAAGTTCA
* *
6271613 TTCTCTTAATATTTTATAAGTTC
1 TTCTCCTAAAATTTTATAAGTTC
6271636 GTCCCTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (24 bp):
TTCTCCTAAAATTTTATAAGTTCA
Found at i:6271646 original size:24 final size:23
Alignment explanation
Indices: 6271594--6271648 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
6271584 ATTTCTTCTC
* *
6271594 CTAAAATTTTATAAGTTCATTCT
1 CTAATATTTTATAAGTTCATCCT
*
6271617 CTTAATATTTTATAAGTTCGTCCCT
1 C-TAATATTTTATAAGTTCAT-CCT
6271642 CTAATAT
1 CTAATAT
6271649 AAAATCATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 23 0.85
25 3 0.11
ACGTcount: A:0.31, C:0.16, G:0.05, T:0.47
Consensus pattern (23 bp):
CTAATATTTTATAAGTTCATCCT
Found at i:6275203 original size:18 final size:18
Alignment explanation
Indices: 6275155--6275204 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
6275145 TTTAAAAAGA
**
6275155 TAAAATTATTTTAAAAAT
1 TAAAATTAAATTAAAAAT
*
6275173 TAAAATATAAATTAACAAT
1 TAAAAT-TAAATTAAAAAT
6275192 TAAAATTAAATTA
1 TAAAATTAAATTA
6275205 TTAAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTAAATTAAAAAT
Found at i:6275228 original size:11 final size:9
Alignment explanation
Indices: 6275199--6275233 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
6275189 AATTAAAATT
6275199 AAATTATTA
1 AAATTATTA
6275208 AAATTATTA
1 AAATTATTA
6275217 AATATATATTA
1 AA-AT-TATTA
6275228 AAATTA
1 AAATTA
6275234 CTCGAACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 13 0.54
10 4 0.17
11 7 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAATTATTA
Found at i:6276296 original size:32 final size:31
Alignment explanation
Indices: 6276260--6276336 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
6276250 TCGGGCCGTG
*
6276260 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
6276292 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
6276323 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
6276337 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Done.